scholarly journals CRISPR-Based Methods for Caenorhabditis elegans Genome Engineering

Genetics ◽  
2016 ◽  
Vol 202 (3) ◽  
pp. 885-901 ◽  
Author(s):  
D. J. Dickinson ◽  
B. Goldstein
Keyword(s):  
Caenorhabditis Elegans ◽  
Genome Engineering ◽  
Caenorhabditis Elegans Genome

A Deficiency Screen for Zygotic Loci Required for Establishment and Patterning of the Epidermis in Caenorhabditis elegans

Genetics ◽  
1997 ◽  
Vol 146 (1) ◽  
pp. 185-206 ◽  
Author(s):  
Rebecca M Terns ◽  
Peggy Kroll-Conner ◽  
Jiangwen Zhu ◽  
Sooyoun Chung ◽  
Joel H Rothman
Keyword(s):  
Caenorhabditis Elegans ◽  
Cell Types ◽  
Epidermal Cells ◽  
Epidermal Differentiation ◽  
Apparent Effect ◽  
Internal Organs ◽  
C Elegans ◽  
Seam Cell ◽  
Genomic Regions ◽  
Caenorhabditis Elegans Genome

To identify genomic regions required for establishment and patterning of the epidermis, we screened 58 deficiencies that collectively delete at least ∼67% of the Caenorhabditis elegans genome. The epidermal pattern of deficiency homozygous embryos was analyzed by examining expression of a marker specific for one of the three major epidermal cell types, the seam cells. The organization of the epidermis and internal organs was also analyzed using a monoclonal antibody specific for epithelial adherens junctions. While seven deficiencies had no apparent effect on seam cell production, 21 were found to result in subnormal, and five in excess numbers of these cells. An additional 23 deficiencies blocked expression of the seam cell marker, in some cases without preventing cell proliferation. Two deficiencies result in multinucleate seam cells. Deficiencies were also identified that result in subnormal numbers of epidermal cells, hyperfusion of epidermal cells into a large syncytium, or aberrant epidermal differentiation. Finally, analysis of internal epithelia revealed deficiencies that cause defects in formation of internal organs, including circularization of the intestine and bifurcation of the pharynx lumen. This study reveals that many regions of the C. elegans genome are required zygotically for patterning of the epidermis and other epithelia.

scholarly journals How Long Are Long Tandem Repeats? A Challenge for Current Methods of Whole-Genome Sequence Assembly: The Case of Satellites in Caenorhabditis elegans

Genes ◽  
2018 ◽  
Vol 9 (10) ◽  
pp. 500
Author(s):  
Juan A. Subirana ◽  
Xavier Messeguer
Keyword(s):  
Caenorhabditis Elegans ◽  
Sanger Sequencing ◽  
Tandem Repeats ◽  
Whole Genome Sequence ◽  
Nanopore Sequencing ◽  
Original Sequence ◽  
Genome Sequence Assembly ◽  
Long Read ◽  
Genomic Regions ◽  
Caenorhabditis Elegans Genome

Repetitive genome regions have been difficult to sequence, mainly because of the comparatively small size of the fragments used in assembly. Satellites or tandem repeats are very abundant in nematodes and offer an excellent playground to evaluate different assembly methods. Here, we compare the structure of satellites found in three different assemblies of the Caenorhabditis elegans genome: the original sequence obtained by Sanger sequencing, an assembly based on PacBio technology, and an assembly using Nanopore sequencing reads. In general, satellites were found in equivalent genomic regions, but the new long-read methods (PacBio and Nanopore) tended to result in longer assembled satellites. Important differences exist between the assemblies resulting from the two long-read technologies, such as the sizes of long satellites. Our results also suggest that the lengths of some annotated genes with internal repeats which were assembled using Sanger sequencing are likely to be incorrect.

The genetic and RFLP characterization of the left end of linkage group III in Caenorhabditis elegans

Genome ◽  
1993 ◽  
Vol 36 (4) ◽  
pp. 712-724 ◽  
Author(s):  
Dave Pilgrim
Keyword(s):  
Caenorhabditis Elegans ◽  
Linkage Group ◽  
Genetic Map ◽  
Physical Map ◽  
Group Iii ◽  
C Elegans ◽  
Genomic Regions ◽  
Caenorhabditis Elegans Genome ◽  
Selection Of

A genetic approach was taken to identify new transposable element Tc1 -dependent polymorphisms on the left end of linkage group III in the nematode Caenorhabditis elegans. The cloning of the genomic DNA surrounding the Tc1 allowed the selection of overlapping clones (from the collection being used to assemble the physical map of the C. elegans genome). A contig of approximately 600–800 kbp in the region has been identified, the genetic map of the region has been refined, and 10 new RFLPs as well as at least four previously characterized genetic loci have been positioned onto the physical map, to the resolution of a few cosmids. This analysis demonstrated the ability to combine physical and genetic mapping for the rapid analysis of large genomic regions (0.5–1 Mbp) in genetically amenable eukaryotes.Key words: Caenorhabditis elegans, genome analysis, RFLP, physical map, genetic map.

Cloning within the unc-43 to unc-31 interval (linkage group IV) of the Caenorhabditis elegans genome using Tc1 linkage selection

1985 ◽  
Vol 27 (4) ◽  
pp. 457-466 ◽  
Author(s):  
D. L. Baillie ◽  
K. A. Beckenbach ◽  
A. M. Rose
Keyword(s):  
Caenorhabditis Elegans ◽  
Restriction Fragment ◽  
Fragment Length ◽  
Region Of Interest ◽  
Group Iv ◽  
Molecular Organization ◽  
C Elegans ◽  
The Right ◽  
Caenorhabditis Elegans Genome ◽  
Restriction Fragment Length

The region around the twitcher gene, unc-22, flanked by unc-43 on the left and by unc-31 on the right, has been intensively studied in our laboratory over the period of the last 8 years. In this paper we describe the identification and isolation of probes specific for several restriction fragment length differences (RFLDs) which lie within this region. Many RFLDs in Caenorhabditis elegans are caused by the insertion of a transposable element, Tc1. The method we used involved the isolation of Tc1-containing genomic fragments. These were recovered from a λgt 10 library of DNA from a specially constructed genetic strain containing the unc-43 to unc-31 interval from the BO strain and the rest of the genome from N2. Because the BO strain is rich in Tc1 insertion sites and the N2 strain has few, the majority of Tc1-bearing genomic fragments in the constructed strain were derived from the unc-22 region. Of nine such Tc1-bearing genomic fragments isolated, six were found which mapped within the region of interest. The 350 kilobases of genomic sequences isolated as a result of these studies are being used to study the molecular organization of this region. The method described here for Tc1 linkage selection is one that is rapid, general, and may be targeted to any genetically characterized region of the C. elegans genome.Key words: Tc1, unc-22, restriction fragment length differences, Caenorhabditis elegans, linkage selection.

scholarly journals Reliable CRISPR/Cas9 Genome Engineering in Caenorhabditis elegans Using a Single Efficient sgRNA and an Easily Recognizable Phenotype

2017 ◽  
Vol 7 (5) ◽  
pp. 1429-1437 ◽  
Author(s):  
Sonia El Mouridi ◽  
Claire Lecroisey ◽  
Philippe Tardy ◽  
Marine Mercier ◽  
Alice Leclercq-Blondel ◽  
...  
Keyword(s):  
Caenorhabditis Elegans ◽  
Genome Engineering
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